The objective of the study was to examine the influence of encapsulated Lactobacillus casei 01 combining with two types of pressurized-purple-rice drinks on colonizing the colon using a simulator of the human intestinal microbial ecosystem. Subsequently, the metabolic products of colon bacteria and various microflora were determined. The finding revealed that acetate which was the predominant short-chain fatty acid (SCFA) was found in both proximal and distal colons, while the combination of encapsulated L. casei 01 and germinated-purple-rice drinks gave rise to highest formation of SCFA. Significant impact of rice drinks could be observed on reducing ammonia production. The quantitative polymerase chain reaction analysis demonstrated that encapsulated L. casei 01 and encapsulated L. casei 01 plus rice drinks markedly increased concentration of colon lactobacilli and bifidobacteria by 2 and 1 log 16S rRNA gene copies/mL, respectively. On the contrary, undesirable bacteria such as clostridia and coliforms were significantly reduced with the influence of encapsulated L. casei 01 plus purple-rice drinks.